丹参基因组SSR位点的特征分析及引物开发  

Characterization and Primer Design for Simple Sequence Repeat Loci in Salvia miltorrhiza Genome

作　　者：徐海滨[1] 钱俊[1] 汪波[1] 孙超[1] 谢丽芳 宋经元[1] 

机构地区：[1]中国医学科学院北京协和医学院药用植物研究所,北京100193 [2]中国医学科学院高性能计算平台,北京100730

出　　处：《世界科学技术-中医药现代化》2013年第3期367-370,共4页Modernization of Traditional Chinese Medicine and Materia Medica-World Science and Technology

基　　金：科学技术部国家科技支撑计划(2012BAI29B01):基于本草基因组的中药材活性成分生合成及育种示范研究,负责人:宋经元;教育部长江学者与创新团队发展计划(IRT1150):中药资源学,负责人:陈士林

摘　　要：丹参为唇形科鼠尾草属多年生落叶开花植物,以根与根茎部位入药,广泛用于多种疾病的治疗。本研究采用生物信息学方法,从丹参基因组框架图序列中发掘出4 832个长度超过40 bp的基因组SSR位点。结果表明,二核苷酸重复基元和三核苷酸重复基元是构成丹参基因组SSR位点的主要类型,分别占全部SSR位点总数的37.3%和61.3%。此外,富含A/T碱基的SSR位点,包括AT/TA、AAT/ATT、ATA/TAT、TAA/TTA,分别占全部SSR位点总数的30.5%,21.6%,17.1%,20.4%,在数量上明显高于其他类型。以基因组SSR位点为基础,共设计基因组SSR引物序列1 079对。这些引物可用于基因组多样性分析、遗传图谱构建、分子标记筛选等工作,为后期丹参群体遗传学与基因组学研究奠定基础。Salvia miltorrhiza Bge.is a perennial deciduous flowering plant.Its medicinal root and rhizomes part is widely used in the treatment of various diseases.In this study,bioinformatics analysis was performed to identify 4832 genome SSR loci with length longer than or equal to 40 bp from the draft genome assembly of S.miltorrhiza.The results showed that the dinucleotide repeat motifs and trinucleotide repeat motifs constitute the main types of genome SSR loci,accounting for 37.3% and 61.3% respectively.SSR types enriched with A/T bases showed significantly higher abundance than other types,including AT/TA AAT/ATT,ATA/TAT,TAA/TTA,accounting for 30.5%,21.6%,17.1%,20.4% of the total number of SSR loci,respectively.1079 primer pairs were designed for these genome SSR loci.These primers can be used for genomic diversity analysis,genetic map construction,genetic marker screening.These data could lay the foundation for population genetics and genomics research of S.miltorrhiza.

关 键 词：丹参 简单重复序列 引物设计 

分 类 号：R282[医药卫生—中药学]